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In January 2021, Senegal reported the emergence of highly pathogenic avian influenza virus A(H5N1), which was detected on a poultry farm in Thies, Senegal, and in great white pelicans in the Djoudj National Bird Sanctuary. We report evidence of new transcontinental spread of H5N1 from Europe toward Africa.

Understanding biotic changes that occur alongside climate change constitute a research priority of global significance. Here, we address a plant pathogen that poses a serious threat to life on natural oases, where climate change is already taking a toll and severely impacting human subsistence. Fusarium oxysporum f. sp. albedinis is a pathogen that causes dieback disease on date palms, a tree that provides several critical ecosystem services in natural oases; and consequently, of major importance in this vulnerable habitat. Here, we assess the current state of global pathogen spread, we annotate the genome of a sequenced pathogen strain isolated from the native range and we analyse its in silico secretome. The palm dieback pathogen secretes a large arsenal of effector candidates including a variety of toxins, a distinguished profile of secreted in xylem proteins (SIX) as well as an expanded protein family with an N-terminal conserved motif [SG]PC[KR]P that could be involved in interactions with host membranes. Using agrobiodiversity as a strategy to decrease pathogen infectivity, while providing short term resilient solutions, seems to be widely overcome by the pathogen. Hence, the urgent need for future mechanistic research on the palm dieback disease and a better understanding of pathogen genetic diversity.

Microsatellite markers are widely used in population genetics and breeding. Despite the economic significance of yams in developing countries, there is a paucity of microsatellite markers, and as of now, no comprehensive microsatellite marker database exists. In this study, we conducted genome‐wide microsatellite marker development across four yam species, identified cross‐species transferable markers, and designed an easy‐to‐use web portal for the yam researchers. The screening of Dioscorea alata, Dioscorea rotundata, Dioscorea dumetorum, and Dioscorea zingiberensis genomes resulted in 318,713, 322,501, 307,040, and 253,856 microsatellites, respectively. Mono‐, di‐, and tri‐nucleotides were the most important types of repeats in the different species, and a total of 864,128 primer pairs were designed. Furthermore, we identified 1170 cross‐species transferable microsatellite markers. Among them, 17 out of 18 randomly selected were experimentally validated with good discriminatory power, regardless of the species and ploidy levels. Ultimately, we created and deployed a dynamic Yam Microsatellite Markers Database (Y2MD) available at https://y2md.ucad.sn/. Y2MD is embedded with various useful tools such as JBrowse, Blast, insilicoPCR, and SSR Finder to facilitate the exploitation of microsatellite markers in yams. This study represents the first comprehensive microsatellite marker mining across several yam species and will contribute to advancing yam genetic research and marker‐assisted breeding. The released user‐friendly database constitutes a valuable platform for yam researchers. Core Ideas Whole genome assemblies of the four yam species were screened for the detection of microsatellites. A set of 1170 cross‐species transferable microsatellite markers were identified. An experimentally validated subset of 17 markers has shown consistent discriminatory power with respect to species and ploidy levels. A user‐friendly and dynamic web portal, the Yam Microsatellite Markers Database (Y2MD), has been developed and made freely available at https://y2md.ucad.sn/. The database includes a number of useful tools such as JBrowse, insilicoPCR, SSRFinder, and Blast. Plain Language Summary Yams (Dioscorea spp.) are vital for developing economies, yet improved varieties are slow to emerge. To accelerate breeding, our study addressed the scarcity of microsatellite markers in yams. We developed 864,128 primer pairs, identifying 1170 transferable markers across species. The validation of 17 markers proved functionality irrespective of species or ploidy. These resources are housed in an online database, fostering collaboration and advancing yam genetic studies and marker‐assisted breeding.

Microsatellite markers are widely used in population genetics and breeding. Despite the economic significance of yams in developing countries, there is a paucity of microsatellite markers, and as of now, no comprehensive microsatellite marker database exists. In this study, we conducted genome-wide microsatellite marker development across four yam species, identified cross-species transferable markers, and designed an easy-to-use web portal for the yam researchers. The screening of Dioscorea alata, Dioscorea rotundata, Dioscorea dumetorum, and Dioscorea zingiberensis genomes resulted in 318,713, 322,501, 307,040, and 253,856 microsatellites, respectively. Mono-, di-, and tri-nucleotides were the most important types of repeats in the different species, and a total of 864,128 primer pairs were designed. Furthermore, we identified 1170 cross-species transferable microsatellite markers. Among them, 17 out of 18 randomly selected were experimentally validated with good discriminatory power, regardless of the species and ploidy levels. Ultimately, we created and deployed a dynamic Yam Microsatellite Markers Database (Y2MD) available at https://y2md.ucad.sn. Y2MD is embedded with various useful tools such as JBrowse, Blast, insilicoPCR, and SSR Finder to facilitate the exploitation of microsatellite markers in yams. This study represents the first comprehensive microsatellite marker mining across several yam species and will contribute to advancing yam genetic research and marker-assisted breeding. The released user-friendly database constitutes a valuable platform for yam researchers.Plain Language Summary: Yams (Dioscorea spp.) are vital for developing economies, yet improved varieties are slow to emerge. To accelerate breeding, our study addressed the scarcity of microsatellite markers in yams. We developed 864,128 primer pairs, identifying 1170 transferable markers across species. The validation of 17 markers proved functionality irrespective of species or ploidy. These resources are housed in an online database, fostering collaboration and advancing yam genetic studies and marker-assisted breeding.

Microsatellite markers are widely used in population genetics and breeding. Despite the economic significance of yams in developing countries, there is a paucity of microsatellite markers, and as of now, no comprehensive microsatellite marker database exists. In this study, we conducted genome-wide microsatellite marker development across four yam species, identified cross-species transferable markers, and designed an easy-to-use web portal for the yam researchers. The screening of Dioscorea alata, Dioscorea rotundata, Dioscorea dumetorum, and Dioscorea zingiberensis genomes resulted in 318,713, 322,501, 307,040, and 253,856 microsatellites, respectively. Mono-, di-, and tri-nucleotides were the most important types of repeats in the different species, and a total of 864,128 primer pairs were designed. Furthermore, we identified 1170 cross-species transferable microsatellite markers. Among them, 17 out of 18 randomly selected were experimentally validated with good discriminatory power, regardless of the species and ploidy levels. Ultimately, we created and deployed a dynamic Yam Microsatellite Markers Database (Y2MD) available at . Y2MD is embedded with various useful tools such as JBrowse, Blast, insilicoPCR, and SSR Finder to facilitate the exploitation of microsatellite markers in yams. This study represents the first comprehensive microsatellite marker mining across several yam species and will contribute to advancing yam genetic research and marker-assisted breeding. The released user-friendly database constitutes a valuable platform for yam researchers.Whole genome assemblies of the four yam species were screened for the detection of microsatellites.A set of 1170 cross-species transferable microsatellite markers were identified.An experimentally validated subset of 17 markers has shown consistent discriminatory power with respect to species and ploidy levels.A user-friendly and dynamic web portal, the Yam Microsatellite Markers Database (Y2MD), has been developed and made freely available at .The database includes a number of useful tools such as JBrowse, insilicoPCR, SSRFinder, and Blast.Yams (Dioscorea spp.) are vital for developing economies, yet improved varieties are slow to emerge. To accelerate breeding, our study addressed the scarcity of microsatellite markers in yams. We developed 864,128 primer pairs, identifying 1170 transferable markers across species. The validation of 17 markers proved functionality irrespective of species or ploidy. These resources are housed in an online database, fostering collaboration and advancing yam genetic studies and marker-assisted breeding.

Background: Microsatellite markers represent a low-cost and efficient tool for rapid genotyping as compared to single nucleotide polymorphism markers in laboratories with limited resources. For the economically important yam species widely cultivated in developing countries, very few microsatellite markers are available and no marker database has been developed to date. Herein, we conducted a genome-wide microsatellite marker development among four yam species, identified cross-species transferable markers, and designed an easy-to-use web portal for the yam breeder community. Results: The screening of yam genomes resulted in 318,713; 322,501; 307,040 and 253,856 microsatellites in Dioscorea alata, D. rotundata, D. dumetorum, and D. zingiberensis, respectively. Mono-, di- and tri-nucleotides were the most important types of repeats in the different species and a total of 864,128 primer pairs were designed. Furthermore, we identified 1170 cross-species transferable microsatellite markers. Among them, a subset of 17 markers were experimentally validated with good discriminatory power regarding the species and the ploidy levels. Ultimately, we created and deployed a dynamic Yam Microsatellite Markers Database (Y2MD) available at http://yamdb.42web.io/. Y2MD is embedded with various useful tools such as JBrowse, Blast, insilicoPCR, and SSR Finder to facilitate the exploitation of microsatellite markers in yams. Conclusions: The present work is the first comprehensive microsatellite marker mining across several yam species and will contribute to advance yam genetic research and marker-assisted breeding. The released user-friendly database constitutes a valuable platform for yam breeders, especially those in developing countries. Keywords: genotyping; Dioscoreacea; database; microsatellite; transferable markersCompeting Interest StatementThe authors have declared no competing interest.

Background Chikungunya fever (CHIK) caused by the mosquito-borne chikungunya virus (CHIKV) and transmitted by Aedes (Ae.) mosquitoes, remains a public health burden throughout the tropics. During the CHIK outbreak in southeastern Senegal in August 2023, an entomologic investigation was conducted to identify the vector(s) and characterize the virus strains. Methods Adult mosquitoes were collected indoors and outdoors from houses of confirmed CHIK cases and their immediate neighborhoods using Prokopack aspirators and double-net traps and all water containers were inspected for aquatic stages. Mosquito pools were tested for CHIKV by RT-qPCR and positive samples were subjected to whole genome sequencing using Illumina iSeq system. Results Animal watering points, bricks, and tree holes were the most common sites for Ae. aegypti larvae and pupae. While immature Ae. aegypti were found in all affected villages, with Breteau and Container indices exceeding the WHO epidemic thresholds, Ae. furcifer emerged as the most abundant host-seeking species collected in domestic areas. CHIKV was detected in 31 mosquito pools, primarily in Ae. furcifer (22 pools) and only one pool of Ae. aegypti . Other Ae. species accounted for 8 positive pools and Anopheles (An.) gambiae complex, the primary malaria vector, one pool. Phylogenetic analysis confirmed the close relationship between 2023 CHIKV strains circulating in humans and mosquitoes, and those responsible for the 2015 outbreak. Conclusions Our study highlights the urgent need to include sylvatic mosquitoes in surveillance and control programs that until now have mainly focused on Ae. aegypti . Moreover, the potential role of An. gambiae in the CHIKV transmission in Senegal warrants further investigation.

While WHO recently recommended universal parasitological confirmation of suspected malaria prior to treatment, debate has continued as to whether wide-scale use of rapid diagnostic tests (RDTs) can achieve this goal. Adherence of health service personnel to RDT results has been poor in some settings, with little impact on anti-malarial drug consumption. The Senegal national malaria control programme introduced universal parasite-based diagnosis using malaria RDTs from late 2007 in all public health facilities. This paper assesses the impact of this programme on anti-malarial drug consumption and disease reporting. Nationally-collated programme data from 2007 to 2009 including malaria diagnostic outcomes, prescription of artemisinin-based combination therapy (ACT) and consumption of RDTs in public health facilities, were reviewed and compared. Against a marked seasonal variation in all-cause out-patient visits, non-malarial fever and confirmed malaria, parasite-based diagnosis increased nationally from 3.9% of reported malaria-like febrile illness to 86.0% over a 3 year period. The prescription of ACT dropped throughout this period from 72.9% of malaria-like febrile illness to 31.5%, reaching close equivalence to confirmed malaria (29.9% of 584,873 suspect fever cases). An estimated 516,576 courses of inappropriate ACT prescription were averted. The data indicate high adherence of anti-malarial prescribing practice to RDT results after an initial run-in period. The large reduction in ACT consumption enabled by the move from symptom-based to parasite-based diagnosis demonstrates that effective roll-out and use of malaria RDTs is achievable on a national scale through well planned and structured implementation. While more detailed information on management of parasite-negative cases is required at point of care level to assess overall cost-benefits to the health sector, considerable cost-savings were achieved in ACT procurement. Programmes need to be allowed flexibility in management of these funds to address increases in other programmatic costs that may accrue from improved diagnosis of febrile disease.

In Senegal, the main vector control strategies include indoor residual spraying (IRS) and the distribution of insecticide-treated nets (ITNs). However, drugs and insecticides resistance have become a major challenge in the fight against malaria transmission. Addressing the problem of escalating resistance is vital to maintaining progress towards malaria elimination, which has stalled in recent years. New formulations belonging to the neonicotinoid class, clothianidin, have been developed and is now being used for malaria vector control through IRS. The residual efficacy of clothianidin-treated walls was assessed monthly using WHO cone bioassays. Five houses in each of the two treated villages were evaluated, while one untreated house served as a control. In the experimental huts, a total of six huts, three in banco (mud) and three in cement, were evaluated on a monthly basis. Three cones were installed on three walls of each sprayed house at heights of 0.5 m, 1 m and 1.5 m above the ground, and three additional cones were placed in the control house. Ten female Anopheles coluzzii mosquitoes, aged between 3 and 5 days and derived from a laboratory-susceptible strain, were exposed in each cone for 30 min. After exposure, the mosquitoes were transferred to cups and mortality rates were recorded up to four days after exposure. Results demonstrate high efficacy of SumiShield 50WG on mud and cement substrates, residual activity for up to twelve months in experimental huts and eight months under field conditions. In experimental huts, the 96 h mortality rate of the susceptible mosquito strain remained at 100% throughout the study, except in months ten and twelve for mud-walled huts, and months six and ten for cement-walled huts, where mortality rates were 98.33%, 99.16%, 95.68%, and 97.52%, respectively. In the field sites of Bandafassi and Tomboronkoto, the 72 h mortality rate of the susceptible strain remained consistently at 100% over the eight-month period. Clothianidin, a neonicotinoid insecticide, has not yet shown resistance in malaria vectors in Senegal. SumiShield 50WG is effective for resistance management through a rotation strategy using insecticides with different modes of action across spray cycles.